The objective of this proposal is the development and optimization of methodologies which are designed to generate a novel, low-cost, high- throughput method of genotyping using single nucleotide polymorphisms (SNPs) as genetic markers. This method relies on the innovative use of reduced complexity genomes, microarray technology and allele-specific oligonucleotide (ASO) hybridization techniques to allow the rapid and efficient identification of SNPs and the simultaneous genotyping of thousands of individuals. This method allows the analysis of over 100 SNPs from a single PCR reaction. The development of such a SNP-based genotyping method will eventually allow the genetic dissection of complex traits such as diabetes and asthma. Preliminary experiments have generated a reduced complexity genome that has allowed the efficient identification of over 50 SNPs which have a 50% success rate in ASO hybridization on DNA derived from multiple CEPH families. This proposal will allow the identification of a maximum number of SNPs having a greater than 80% success rate in ASO hybridizations. Additionally this proposal is designed to identify approximately 100 unique SNPs and determine their genomic map location and allele frequency. PROPOSED COMMERCIAL APPLICATIONS: A high throughput, low-cost genotyping technology will support large population studies to genetically dissect complex traits such as diabetes, obesity and heart disease. This has significant commercial applications for understanding and diagnosis of many common diseases as well as the discovery of noel therapeutic treatments. This technology is ideal for pharmacogenomic studies to identify candidate populations likely to benefit from noel therapeutic agents. Additionally it offers a rapid, low- cost approach for digital DNA fingerprinting for military and criminal identification and forensic applications.